Multiple sequence alignment - TraesCS5B01G179400

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS5B01G179400 chr5B 100.000 2288 0 0 1 2288 327194480 327196767 0.000000e+00 4226.0
1 TraesCS5B01G179400 chr5B 86.382 1733 177 26 8 1707 470217246 470218952 0.000000e+00 1838.0
2 TraesCS5B01G179400 chr5B 85.986 1734 184 30 8 1703 477756411 477758123 0.000000e+00 1801.0
3 TraesCS5B01G179400 chr5B 89.910 892 76 6 1 883 565795997 565796883 0.000000e+00 1136.0
4 TraesCS5B01G179400 chr5B 97.099 586 17 0 1703 2288 327438958 327439543 0.000000e+00 989.0
5 TraesCS5B01G179400 chr3A 90.982 1741 118 15 1 1704 418765675 418763937 0.000000e+00 2309.0
6 TraesCS5B01G179400 chr4D 90.104 1738 131 19 1 1701 421048651 421046918 0.000000e+00 2218.0
7 TraesCS5B01G179400 chr7D 89.902 1743 136 10 1 1707 432740558 432738820 0.000000e+00 2207.0
8 TraesCS5B01G179400 chr4A 89.937 1739 137 10 1 1703 327748389 327746653 0.000000e+00 2207.0
9 TraesCS5B01G179400 chr1A 89.564 1744 134 22 1 1704 327011933 327010198 0.000000e+00 2169.0
10 TraesCS5B01G179400 chr2B 89.304 1739 139 19 10 1707 713704748 713703016 0.000000e+00 2137.0
11 TraesCS5B01G179400 chr2B 90.283 1132 92 6 594 1707 636460237 636459106 0.000000e+00 1465.0
12 TraesCS5B01G179400 chr2B 90.154 518 40 6 1198 1707 612692317 612691803 0.000000e+00 664.0
13 TraesCS5B01G179400 chr6B 88.882 1736 146 20 7 1707 81981056 81982779 0.000000e+00 2093.0
14 TraesCS5B01G179400 chr6B 85.979 1726 187 21 34 1714 452621557 452619842 0.000000e+00 1796.0
15 TraesCS5B01G179400 chr6B 86.903 1298 135 19 417 1704 113986297 113987569 0.000000e+00 1423.0
16 TraesCS5B01G179400 chr1B 88.032 1738 158 23 10 1707 192470117 192468390 0.000000e+00 2012.0
17 TraesCS5B01G179400 chr6D 87.873 1707 165 19 7 1685 469235208 469236900 0.000000e+00 1967.0
18 TraesCS5B01G179400 chr5D 87.730 1736 124 24 1 1699 460216213 460217896 0.000000e+00 1943.0
19 TraesCS5B01G179400 chr5D 93.909 591 30 2 1703 2288 288152347 288152936 0.000000e+00 887.0
20 TraesCS5B01G179400 chr5D 93.739 591 32 1 1703 2288 288133992 288134582 0.000000e+00 881.0
21 TraesCS5B01G179400 chr2A 87.052 1730 175 18 7 1706 779811858 779813568 0.000000e+00 1908.0
22 TraesCS5B01G179400 chr2D 86.890 1434 141 17 298 1707 469162163 469163573 0.000000e+00 1563.0
23 TraesCS5B01G179400 chr5A 89.912 912 83 6 2 904 392040582 392041493 0.000000e+00 1166.0
24 TraesCS5B01G179400 chr5A 94.397 464 20 1 1831 2288 380823750 380824213 0.000000e+00 708.0
25 TraesCS5B01G179400 chr5A 92.941 255 18 0 2034 2288 380794257 380794511 2.780000e-99 372.0
26 TraesCS5B01G179400 chr5A 93.671 158 10 0 1834 1991 380794103 380794260 1.060000e-58 237.0
27 TraesCS5B01G179400 chr5A 89.474 76 2 1 1765 1834 380790481 380790556 8.700000e-15 91.6
28 TraesCS5B01G179400 chr1D 90.338 859 68 3 1 850 429020170 429021022 0.000000e+00 1112.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS5B01G179400 chr5B 327194480 327196767 2287 False 4226.000000 4226 100.000000 1 2288 1 chr5B.!!$F1 2287
1 TraesCS5B01G179400 chr5B 470217246 470218952 1706 False 1838.000000 1838 86.382000 8 1707 1 chr5B.!!$F3 1699
2 TraesCS5B01G179400 chr5B 477756411 477758123 1712 False 1801.000000 1801 85.986000 8 1703 1 chr5B.!!$F4 1695
3 TraesCS5B01G179400 chr5B 565795997 565796883 886 False 1136.000000 1136 89.910000 1 883 1 chr5B.!!$F5 882
4 TraesCS5B01G179400 chr5B 327438958 327439543 585 False 989.000000 989 97.099000 1703 2288 1 chr5B.!!$F2 585
5 TraesCS5B01G179400 chr3A 418763937 418765675 1738 True 2309.000000 2309 90.982000 1 1704 1 chr3A.!!$R1 1703
6 TraesCS5B01G179400 chr4D 421046918 421048651 1733 True 2218.000000 2218 90.104000 1 1701 1 chr4D.!!$R1 1700
7 TraesCS5B01G179400 chr7D 432738820 432740558 1738 True 2207.000000 2207 89.902000 1 1707 1 chr7D.!!$R1 1706
8 TraesCS5B01G179400 chr4A 327746653 327748389 1736 True 2207.000000 2207 89.937000 1 1703 1 chr4A.!!$R1 1702
9 TraesCS5B01G179400 chr1A 327010198 327011933 1735 True 2169.000000 2169 89.564000 1 1704 1 chr1A.!!$R1 1703
10 TraesCS5B01G179400 chr2B 713703016 713704748 1732 True 2137.000000 2137 89.304000 10 1707 1 chr2B.!!$R3 1697
11 TraesCS5B01G179400 chr2B 636459106 636460237 1131 True 1465.000000 1465 90.283000 594 1707 1 chr2B.!!$R2 1113
12 TraesCS5B01G179400 chr2B 612691803 612692317 514 True 664.000000 664 90.154000 1198 1707 1 chr2B.!!$R1 509
13 TraesCS5B01G179400 chr6B 81981056 81982779 1723 False 2093.000000 2093 88.882000 7 1707 1 chr6B.!!$F1 1700
14 TraesCS5B01G179400 chr6B 452619842 452621557 1715 True 1796.000000 1796 85.979000 34 1714 1 chr6B.!!$R1 1680
15 TraesCS5B01G179400 chr6B 113986297 113987569 1272 False 1423.000000 1423 86.903000 417 1704 1 chr6B.!!$F2 1287
16 TraesCS5B01G179400 chr1B 192468390 192470117 1727 True 2012.000000 2012 88.032000 10 1707 1 chr1B.!!$R1 1697
17 TraesCS5B01G179400 chr6D 469235208 469236900 1692 False 1967.000000 1967 87.873000 7 1685 1 chr6D.!!$F1 1678
18 TraesCS5B01G179400 chr5D 460216213 460217896 1683 False 1943.000000 1943 87.730000 1 1699 1 chr5D.!!$F3 1698
19 TraesCS5B01G179400 chr5D 288152347 288152936 589 False 887.000000 887 93.909000 1703 2288 1 chr5D.!!$F2 585
20 TraesCS5B01G179400 chr5D 288133992 288134582 590 False 881.000000 881 93.739000 1703 2288 1 chr5D.!!$F1 585
21 TraesCS5B01G179400 chr2A 779811858 779813568 1710 False 1908.000000 1908 87.052000 7 1706 1 chr2A.!!$F1 1699
22 TraesCS5B01G179400 chr2D 469162163 469163573 1410 False 1563.000000 1563 86.890000 298 1707 1 chr2D.!!$F1 1409
23 TraesCS5B01G179400 chr5A 392040582 392041493 911 False 1166.000000 1166 89.912000 2 904 1 chr5A.!!$F2 902
24 TraesCS5B01G179400 chr5A 380790481 380794511 4030 False 233.533333 372 92.028667 1765 2288 3 chr5A.!!$F3 523
25 TraesCS5B01G179400 chr1D 429020170 429021022 852 False 1112.000000 1112 90.338000 1 850 1 chr1D.!!$F1 849

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
953 1017 0.754217 CATGAGGATGGTGGCCCAAG 60.754 60.0 0.0 0.0 46.04 3.61 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1818 1969 1.730064 CCACTTTCCGGATAACGTGTG 59.27 52.381 4.15 4.98 42.24 3.82 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
131 138 2.283604 TACGACAGCCTGGCTCCA 60.284 61.111 20.49 0.00 36.40 3.86
152 159 2.513204 CCCTCACTGGCATCTGCG 60.513 66.667 0.00 0.00 43.26 5.18
274 287 4.228824 AGTTCTTGTACTTGGACCACCTA 58.771 43.478 0.00 0.00 37.04 3.08
288 310 1.336887 CCACCTATTAGCGTCATCGGG 60.337 57.143 0.00 0.00 37.56 5.14
293 315 1.048601 ATTAGCGTCATCGGGGACAT 58.951 50.000 7.88 0.00 37.66 3.06
308 330 1.133699 GGACATCCTGATTCATGGCCA 60.134 52.381 8.56 8.56 46.44 5.36
368 390 5.710099 GGGTTAGGAATCAACATCTTCAACA 59.290 40.000 0.00 0.00 0.00 3.33
373 395 4.919754 GGAATCAACATCTTCAACACTTGC 59.080 41.667 0.00 0.00 0.00 4.01
406 428 2.773993 TGAGCACTGCATCAGATTCA 57.226 45.000 3.30 0.00 35.18 2.57
536 572 2.856988 AAGGGAAGGGGTTGGCGA 60.857 61.111 0.00 0.00 0.00 5.54
544 586 2.742116 GGGGTTGGCGATGGAGCTA 61.742 63.158 0.00 0.00 37.29 3.32
618 667 3.053826 AGGGGGTGGGTAAGTAATGATC 58.946 50.000 0.00 0.00 0.00 2.92
626 675 2.367567 GGTAAGTAATGATCGGCAGGGA 59.632 50.000 0.00 0.00 0.00 4.20
674 727 1.277557 GGAAGAGTGACAGTCATGCCT 59.722 52.381 6.51 0.00 0.00 4.75
758 811 1.676006 TGCAGATCGACGAGAGCAATA 59.324 47.619 16.15 0.00 37.82 1.90
898 960 2.419198 GACGAGCGCATGGAGGAT 59.581 61.111 11.47 0.00 0.00 3.24
942 1006 2.160721 ACGACCACTACCATGAGGAT 57.839 50.000 0.00 0.00 38.69 3.24
953 1017 0.754217 CATGAGGATGGTGGCCCAAG 60.754 60.000 0.00 0.00 46.04 3.61
957 1021 1.217057 AGGATGGTGGCCCAAGTCAT 61.217 55.000 0.00 0.00 46.04 3.06
1226 1293 2.231478 AGGTCATCATCTTTGACGACGT 59.769 45.455 0.00 0.00 44.11 4.34
1244 1311 0.598065 GTTGGCATTGAGGTGGTCAC 59.402 55.000 0.00 0.00 33.71 3.67
1257 1324 2.258726 GGTCACCAAGTGCGGGAAC 61.259 63.158 0.00 0.00 32.98 3.62
1260 1327 2.674563 TCACCAAGTGCGGGAACCAG 62.675 60.000 0.00 0.00 39.87 4.00
1320 1387 6.011122 ACCTCCTTCCTAAGTACTATCGAA 57.989 41.667 0.00 0.00 0.00 3.71
1377 1460 6.710597 ACTATCGTTATGATGTGTGGTACT 57.289 37.500 0.00 0.00 37.99 2.73
1378 1461 7.812690 ACTATCGTTATGATGTGTGGTACTA 57.187 36.000 0.00 0.00 37.99 1.82
1416 1523 7.394816 ACTATGTTGTTAAGTAGTGGATGCTT 58.605 34.615 0.00 0.00 37.61 3.91
1553 1663 3.561143 AGGTTTGTCCACTAACATGCAA 58.439 40.909 0.00 0.00 39.02 4.08
1567 1678 1.122227 ATGCAAGCAACCAAACACCT 58.878 45.000 0.00 0.00 0.00 4.00
1675 1819 4.272489 AGAAGGTTATGCAATGCAGCTAA 58.728 39.130 14.98 5.60 43.65 3.09
1688 1833 3.021695 TGCAGCTAATGTAGACTACGGT 58.978 45.455 8.09 1.14 0.00 4.83
1721 1866 0.749649 CCTAGCCTCGCACATCTCTT 59.250 55.000 0.00 0.00 0.00 2.85
1727 1872 1.391485 CCTCGCACATCTCTTTGAACG 59.609 52.381 0.00 0.00 0.00 3.95
1730 1875 1.463034 CGCACATCTCTTTGAACGCAG 60.463 52.381 0.00 0.00 0.00 5.18
1738 1883 2.964924 CTTTGAACGCAGCGCAACGT 62.965 55.000 20.08 20.08 46.07 3.99
1756 1901 1.002468 CGTTTCTTCCTGCAGTTGTGG 60.002 52.381 13.81 0.00 0.00 4.17
1774 1919 2.434331 CCCCACAGCCTTTTCGGA 59.566 61.111 0.00 0.00 33.16 4.55
1818 1969 1.551883 ACCATACCCTTGTACGTGACC 59.448 52.381 0.00 0.00 0.00 4.02
1852 5550 3.454375 GAAAGTGGAAACTGACGTCAGA 58.546 45.455 43.55 23.71 46.59 3.27
2037 5740 4.094646 ATCCATGGACGCGGTGCA 62.095 61.111 18.99 8.29 38.41 4.57
2261 5964 2.768344 GGGGCGGATCAAGGAGGA 60.768 66.667 0.00 0.00 0.00 3.71
2268 5971 0.758123 GGATCAAGGAGGAGGCTCTG 59.242 60.000 15.23 4.33 0.00 3.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
131 138 0.037303 CAGATGCCAGTGAGGGTGTT 59.963 55.000 0.00 0.00 38.09 3.32
152 159 0.903236 AAGGAGGAGTAAGAACCGGC 59.097 55.000 0.00 0.00 0.00 6.13
274 287 1.000955 GATGTCCCCGATGACGCTAAT 59.999 52.381 0.00 0.00 38.11 1.73
288 310 1.133699 TGGCCATGAATCAGGATGTCC 60.134 52.381 0.00 0.00 37.40 4.02
293 315 0.749091 CGCTTGGCCATGAATCAGGA 60.749 55.000 22.21 0.00 0.00 3.86
308 330 1.002366 GCAGTCGACATCATTCGCTT 58.998 50.000 19.50 0.00 38.95 4.68
373 395 2.513204 CTCATGAGGGCCACTGCG 60.513 66.667 15.38 0.00 38.85 5.18
420 451 1.813513 CTCGAACTTTGGCTCCATGT 58.186 50.000 0.00 0.00 0.00 3.21
618 667 3.833070 ACCTATATTTACTCTCCCTGCCG 59.167 47.826 0.00 0.00 0.00 5.69
626 675 6.010850 TCTCCATCGCACCTATATTTACTCT 58.989 40.000 0.00 0.00 0.00 3.24
674 727 9.840427 GCTTATTGAAGAGCATGTAGTTAAAAA 57.160 29.630 0.00 0.00 38.73 1.94
758 811 2.671070 CACCTCCGTGCCCATCTT 59.329 61.111 0.00 0.00 32.04 2.40
916 980 3.192001 TCATGGTAGTGGTCGTAGTTGTC 59.808 47.826 0.00 0.00 0.00 3.18
953 1017 3.350833 AGGATGACCTTGCAGAAATGAC 58.649 45.455 0.00 0.00 45.36 3.06
1218 1285 0.948623 CCTCAATGCCAACGTCGTCA 60.949 55.000 0.00 0.00 0.00 4.35
1226 1293 3.034924 GTGACCACCTCAATGCCAA 57.965 52.632 0.00 0.00 0.00 4.52
1244 1311 2.672996 CCTGGTTCCCGCACTTGG 60.673 66.667 0.00 0.00 0.00 3.61
1320 1387 5.356751 TCAACGCATAAACCATAAAGCAGAT 59.643 36.000 0.00 0.00 0.00 2.90
1409 1504 4.114058 TCATAAGCAAAGCAAAGCATCC 57.886 40.909 0.00 0.00 0.00 3.51
1416 1523 3.573538 ACCACACATCATAAGCAAAGCAA 59.426 39.130 0.00 0.00 0.00 3.91
1452 1560 1.873591 GTGAGGTTACCAGCACACTTG 59.126 52.381 18.14 0.00 38.52 3.16
1553 1663 1.381056 TGCCAGGTGTTTGGTTGCT 60.381 52.632 0.00 0.00 40.49 3.91
1640 1783 1.428869 ACCTTCTCAACTCAGCCTGT 58.571 50.000 0.00 0.00 0.00 4.00
1675 1819 5.473039 GTGTTTGGTTACCGTAGTCTACAT 58.527 41.667 10.59 0.43 0.00 2.29
1688 1833 0.321830 GCTAGGGGCGTGTTTGGTTA 60.322 55.000 0.00 0.00 0.00 2.85
1721 1866 3.102107 AACGTTGCGCTGCGTTCAA 62.102 52.632 27.27 16.59 46.53 2.69
1727 1872 1.725973 GGAAGAAACGTTGCGCTGC 60.726 57.895 9.73 0.00 0.00 5.25
1730 1875 1.725973 GCAGGAAGAAACGTTGCGC 60.726 57.895 0.00 0.00 0.00 6.09
1738 1883 1.032014 GCCACAACTGCAGGAAGAAA 58.968 50.000 19.93 0.00 0.00 2.52
1756 1901 3.373565 CCGAAAAGGCTGTGGGGC 61.374 66.667 0.00 0.00 41.20 5.80
1774 1919 2.046892 GCTCACTGACATGCGGGT 60.047 61.111 0.00 0.00 0.00 5.28
1818 1969 1.730064 CCACTTTCCGGATAACGTGTG 59.270 52.381 4.15 4.98 42.24 3.82
1852 5550 2.357517 CGTTCCACGGCAGCTTCT 60.358 61.111 0.00 0.00 38.08 2.85


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.